1. Is it academic misconduct if a transcription is not word for word?
2. Is it academic misconduct if I don't write down non-verbal signs such as laughing?
3. Two of the interviewees cancelled meeting in person, and could only do it over the phone, which I did, and recorded. It went perfectly but, do I have to tell my University this?
First, I should mention that I can only speak from my own, limited experience of undertaking qualitative research as part of undergraduate and postgraduate degrees, so I don't claim to speak with any authority or expertise.
Second, the fact that you are conscious of these issues makes me think that you are probably the kind of person whose diligence and care is recognisably demonstrated in their work. Whilst I don't know the details of your course and its regulations etc., I think your worries might be disproportionate. I don't believe that 1 and 2 should be considered instances of academic misconduct; you haven't fabricated or misrepresented the collection and presentation of your data. When writing up your methodology, you can include a sub-section on the 'limitations' of your data collection and analysis (and anything else related to your methodology); I think it would be reasonable to disclose the challenge of verbatim translation into English; and what was not recorded in the transcript (i.e., non-verbal signs). You could discuss the implications of these limitations to demonstrate your awareness of the effect they will or could have on the research and your analysis. Essentially, you are upholding your academic integrity by providing an honest account of your decisions and actions.
Regarding the difficulties that resulted in the telephone interviews, again, these can be discussed in a sub-section on limitations (or a section where you discuss your data collection activities). Unless there's some ethical imperative to holding interviews in-person, I don't believe there is a need to tell the university. It's understandable and reasonable that you sought an alternative means of collecting the data - these kinds of issues are inevitable sooner or later. By discussing it in your dissertation, you will be 'telling the university'.
Aside from the guidance of a supervisor or course staff, the criteria for academic misconduct should be set out in faculty/department and/or handbooks and academic regulations documents.